I included point and click atom and bond deletion into a Jmol molecular
editor. This works just fine, but there are some deletion followup issues:
1) minimize addHydrogens is not functional on a multivalent atom that has
atoms deleted or bonds broken.
2) Point 1 is not all that big of an issue because I think user substitution
of the "defective" multivalent by a new identical multivalent atom is really
fairly intuitive. After this swap, minimize addHydrogens does work again,
with one exception...
3) The exception: If the multivalent atom is not connected to any other
multivalent or non-hydrogen atoms, then the atom replacement step above
simply creates a single atom with no hydrogen atoms attached.
By way of example, if I break a C-C bond in cyclohexane, then the terminal
CH2 groups will be rectified by the following swap - i.e. both end C's are
swapped with new C's:
evalRasmol("{atomIndex = _atomPicked}.element = '" + buildAtom +
"';");
evalRasmol("select hydrogen and connected({atomIndex =
_atomPicked});delete selected;");
evalRasmol("minimize addHydrogens;");
evalRasmol("select *;wireframe 0.15; spacefill 23%;boundbox
{*};centerat boundbox;echo Calculating UFF Minimum...;");
evalRasmol("minimize steps 100;");
buildAtom is a global variable that represents the atom being substituted
in.
When I do this, I'm really using jmol.js and the jmolScript() function. By
running this script text through a function of my own before jmolScript(), I
have the ability to define some jmol script commnads of my own from
jmolScript combinations. I'm not suing any of my defined commands above.
Continuing with my example, if I break a methly group off of hexane with the
intent of reconnecting the pieces to form 2-methylpentane, then all is well.
But if I try to rectify the fragments by the swap described above to create
a molecule of methane and a molecule of pentane, then pentane forms, but the
CH3 fragment is reduced to a single carbon atom that cannot be H rectified.
As a point of information, if I break hexane into two CH3CH2CH2 fragments, I
can reconnect the two fragments any way I want. I can also make two separate
molecules of ethane. It appears that breaking off the following groups from
a larger molecule creates the problem described above:
CH3
OH
NH2
SH
Any suggestions?
Otis
--
Otis Rothenberger
http://chemagic.org
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